Anatoly Buchin

Anatoly Buchin
Cajal Neuroscience · Computational Biology

PhD Computational Neuroscience, MS Physics

About

42
Publications
8,703
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228
Citations
Introduction
Hi everybody, my name is Anatoly Buchin, I am a senior computational biologist at Cajal Neuroscience. I use methods of statistics, machine learning and numerical simulations to study the brain function and pathology. Specifically I am interested in single cell genomics, pathologies of the nervous system and biological neural networks. My current projects are related to multimodal neural data analysis and development of novel drug targets against Alzheimer's and Parkinson's diseases.
Additional affiliations
April 2017 - present
Allen Institute for Brain Science
Position
  • Researcher
February 2016 - present
University of Washington Seattle
Position
  • PostDoc Position
February 2013 - June 2015
Ecole Normale Supérieure de Paris
Position
  • Lecturer
Description
  • Introduction into Neuroscience Modeling

Publications

Publications (42)
Article
Full-text available
Significance statement: Ion regulation in the brain is a major determinant of neural excitability. Intracellular chloride in neurons, a partial determinant of the resting potential and the inhibitory reversal potentials, is regulated together with extracellular potassium via kation chloride cotransporters. During temporal lobe epilepsy, the homeos...
Preprint
Full-text available
Gene expression studies suggest that differential ion channel expression contributes to differences in rodent versus human neuronal physiology. We tested whether h-channels more prominently contribute to the physiological properties of human compared to mouse supragranular pyramidal neurons. Single cell/nucleus RNA sequencing revealed ubiquitous HC...
Preprint
Full-text available
The neocortex is disproportionately expanded in human compared to mouse, both in its total volume relative to subcortical structures and in the proportion occupied by supragranular layers that selectively make connections within the cortex and other telencephalic structures. Single-cell transcriptomic analyses of human and mouse cortex show an incr...
Preprint
Full-text available
Temporal lobe epilepsy is the fourth most common neurological disorder with about 40% of patients not responding to pharmacological treatment. Increased cellular loss in the hippocampus is linked to disease severity and pathological phenotypes such as heightened seizure propensity. While the hippocampus is the target of therapeutic interventions su...
Preprint
Full-text available
Identifying the cell types constituting brain circuits is a fundamental question in neuroscience and motivates the generation of taxonomies based on electrophysiological, morphological and molecular single cell properties. Establishing the correspondence across data modalities and understanding the underlying principles has proven challenging. Bio-...
Article
Full-text available
The neocortex is disproportionately expanded in human compared with mouse1,2, both in its total volume relative to subcortical structures and in the proportion occupied by supragranular layers composed of neurons that selectively make connections within the neocortex and with other telencephalic structures. Single-cell transcriptomic analyses of hu...
Article
Full-text available
Temporal lobe epilepsy is the fourth most common neurological disorder with about 40% of patients not responding to pharmacological treatment. Increased cellular loss in the hippocampus is linked to disease severity and pathological phenotypes such as heightened seizure propensity. While the hippocampus is the target of therapeutic interventions su...
Article
Gene expression studies suggest that differential ion channel expression contributes to differences in rodent versus human neuronal physiology. We tested whether h-channels more prominently contribute to the physiological properties of human compared to mouse supragranular pyramidal neurons. Single-cell/nucleus RNA sequencing revealed ubiquitous HC...
Article
Full-text available
Pharmacoresistant epilepsy is a common neurological disorder in which increased neuronal intrinsic excitability and synaptic excitation lead to pathologically synchronous behavior in the brain. In the majority of experimental and theoretical epilepsy models, epilepsy is associated with reduced inhibition in the pathological neural circuits, yet eff...
Preprint
Full-text available
Pharmacoresistant epilepsy is a common neurological disorder in which increased neuronal intrinsic excitability and synaptic excitation lead to pathologically synchronous behavior in the brain. In the majority of experimental and theoretical epilepsy models, epilepsy is associated with reduced inhibition in the pathological neural circuits, yet eff...
Preprint
Full-text available
Gene expression studies suggest that differential ion channel expression contributes to differences in rodent versus human neuronal physiology. We tested whether h-channels more prominently contribute to the physiological properties of human compared to mouse supragranular pyramidal neurons. Single- cell/nucleus RNA sequencing revealed ubiquitous H...
Poster
Full-text available
Pharmacoresistant epilepsy is a common neurological disorder in which the basic mechanisms of neuronal excitability and connection processes lead to pathologically synchronous behavior in the brain [1]. In the majority of experimental and theoretical epilepsy models, epilepsy is associated with reduced inhibition in the pathological neural circuits...
Poster
Full-text available
• Ion regulation in the brain is a major determinant of neural excitability • Intracellular chloride in neurons is regulated together with extracellular potassium by Kation Chloride Cotransporter 2 (KCC2) • During temporal lobe epilepsy, the regulation of intracellular chloride is impaired in the pyramidal cells due to KCC2(-) pathology • Using rea...
Article
Full-text available
Purkinje neurons play an important role in cerebellar computation since their axons are the only projection from the cerebellar cortex to deeper cerebellar structures. They have com- plex internal dynamics, which allow them to fire spontaneously, display bistability, and also to be involved in network phenomena such as high frequency oscillations a...
Data
History dependence of the ISR curve. A. Current injection of 1 s noise waveform periods in a Purkinje cell in a cerebellar slice, as in Fig 1A. B. Firing frequency vs. noise amplitude σ for five different holding currents Iin. C. Current injection of 1 s noise waveform periods in a different cell with a more pronounced bistability. The firing frequ...
Data
ISR and dendrite filtering. A. Experimental determination of dendritic filtering properties. Voltage response of a Purkinje cell (black) to a short current pulse (0.5 ms, 1 nA), fitted with a biexponential function with time constants τm and τc (red). B. Mean firing rate in the experiment and the aEIF model in response to current noise stimulation,...
Data
The effect of dendrites on ISR in Purkinje cells. (DOCX)
Data
ISR in a detailed Purkinje cell model. A. Top, somatic voltage recording from a detailed Purkinje cell model [22] during injection of the noisy current waveform shown at the bottom (similar to the stimulus used in Fig 1A, but with a different range of noise amplitudes). B. Averaged firing frequency (5 simulations) during 1 s noise waveform periods...
Data
Membrane potential distribution during spiking and silent states. A. Membrane potential distributions computed from a somatic whole-cell patch-clamp recording from a Purkinje cell during a stimulus, which evokes transitions between spiking and silent states (Fig 1A). B. Membrane potential distributions in the aEIF model. C. Somatic membrane potenti...
Data
Mutual information and spiking response for high intensity signal input. A. Mutual Information rate of the input and output spike train in the aEIF model when stimulated with 5 Hz signal input. B. Continuous voltage response of the aEIF model when stimulated by 30 pA noise and a Poisson spike train (input amplitude 100 pA, mean frequency 5 Hz, dura...
Article
Full-text available
Experimentally it has been found that around 20% of pyramidal cells in epileptogenic human subiculum do not have KCC2 co-transporter. This pathology leads to the increased chloride level in pyramidal cells, what changes the action of GABA synapses from inhibition to excitation. In this work we propose the single neuron biophysical model to explain...
Thesis
Full-text available
In this thesis we used dynamical systems methods and numericalsimulations to study the mechanisms of epileptic oscillations associated with ionconcentration changes and cerebellar Purkinje cell bimodal behavior. The general issue in this work is the interplay between single neuron intrinsicproperties and synaptic input structure controlling the neu...
Poster
Full-text available
Purkinje cells play an important role in cerebellar computation since their axons are the only projection from the cerebellar cortex to deeper cerebellar structures. They have complex internal dynamics, which allow them to fire spontaneously, display bistability and participate in network phenomena such as high frequency oscillations and travelling...
Poster
Full-text available
Purkinje cells play an important role in cerebellar computation since their axons are the only projection from the cerebellar cortex to deeper cerebellar structures. They have complex internal dynamics, which allow them to fire spontaneously, display bistability and participate in network phenomena such as high frequency oscillations and travelling...
Article
Full-text available
Epilepsy is one of the most common neurological disorders. Seizures in about 40% of patients with temporal lobe epilepsies are pharmaco-resistant [1]. In surgically removed hippocampal tissue from these patients, the KCC2 cotransporter is absent or non-functional in about 20 % of subicular pyramidal cells [2]. KCC2 normally assures the maintenance...
Conference Paper
Full-text available
Abnormal synchronization of neurons is characteristic for the central nervous system in various neurological diseases, particularly in epilepsy. To describe the dynamics of neurons and to identify causes of this behavior it is necessary to use various theoretical models of individual neurons and populations of cells. In this work we present the pop...
Conference Paper
Full-text available
Experimental data reveal the bimodal behavior of Purkinje cells which could be characterized by firing-rate hysteresis in response to current ramp. We propose an adaptive Exponential Integrate-and-Fire neuron (aEIF) model to explain this bimodality. Another phenomenon found in Purkinje cells, inhibition by noise stimuli, so-called Inverse Stochasti...
Article
Full-text available
A firing rate (FR) model for a population of adaptive integrate-and-fire (IF) neurons has been proposed. Unlike known FR models, it describes more precisely the unsteady firing regimes and takes into account the effect of slow potassium currents of spike-time adaptation. Approximations of the adaptive channel conductances are rewritten from voltage...
Article
Full-text available
Synchronization plays important role in generation of brain activity patterns. Experimental data show that neurons demonstrate more reproducible activity for noise-like input than for constant current injection, and that effect can not be reproduced by standard oversimplified Firing-Rate (FR) models. The paper proposes a modification of FR model wh...
Conference Paper
Full-text available
Purkinje neurons play an important role in Cerebellar computation. Their axons are the only projection from the cerebellar cortex to deeper cerebellar structures. These neurons appear to have a type II excitability, which can be revealed by a discontinuity in their F-I curves. This intrinsic membrane property of the Purkinje cells implies bistable...
Conference Paper
Full-text available
It's well known that synchronous activity play important role in generation of quasiperiodic patterns of brain activity. The imitation of the synaptic current by constant shape signal doesn't always lead to reproducible behavior of one neuron for a long time. But the stimulation by noise-like complex shape signal with fixed parameters lead to the l...
Conference Paper
Full-text available
It is well known that synchronous activity play an important role in generation of patterns of brain activity. It has been shown in experimental studies of synchronous activity that neurons demonstrate more reproducible behavior in a response to complex stimuli rather than to constant current injection. In this work we reproduce such experimental r...

Questions

Questions (2)
Question
Hello dear colleagues!
Does any of you know how an effective algorithm to generate a graph with a given degree distribution with fixed number of elements? I developed a couple of them by myself, but they are not efficient enough. I realized that it is not a trivial problem if there are some geometric constrains (graph on cylinder) and fixed number of elements.
Any ideas or relevant references?
Thanks a lot in advance!
Question
Hi everybody,
I am going to use the Mutual Information (MI) and Transfer Entropy (TE) to characterize the functional connectivity between neurons based on Ca traces. There are many options available, but I am concentrated on TE (TE) and MI as the most general. I extract the spike trains from Ca data and then perform the computations on these vectors.
Based on your experience what method requires smaller amount of data for the reliable estimate of functional connectivity, TE or MI?
What is the advantage of TE over MI, apart from the fact that it is the directed measure?
Many thanks to everyone!

Projects

Projects (5)
Project
Modelling of brain dynamics often requires the simplification of the single neuron properties and description of macroscopic behavior of large ensembles of neurons. In this project we are working on the low-dimensional models of neural populations capturing the essential dynamical properties. In particular we study the representation of slow potassium adaptation currents on the population level and the effect of noise-like stimulation on the population dynamics.